Interactive UpSet Plots Using 'plotly'

Creates interactive UpSet-style visualizations for exploring intersections among multiple sets, following the layout of Lex et al. (2014) . 'plotly' widgets combine set-size bars, intersection-size bars, and membership matrices, and can synchronize complete intersection details with an HTML element for copying in 'Quarto', 'R Markdown', and 'Shiny' documents.

upsetly

Interactive UpSet plots with plotly, with intersection details that can be copied easily in HTML documents (Quarto, R Markdown, Shiny).

upsetly focuses on UpSet-style visualization of set intersections (e.g. differential gene lists), and adds JavaScript hooks so that all tooltip text (Intersection, Size, Members, etc.) can be synced into a separate text box for copy‑and‑paste.

Installation

Until the first CRAN release is accepted, install the development version from GitHub:

# install.packages("remotes")
remotes::install_github("Rbunensi/upsetly")

Then load:

library(upsetly)

Basic idea

Given a data frame with:

• one ID column (e.g. gene), and
• several 0/1 (or logical / character) columns indicating membership in sets
  (e.g. comparisons A_vs_B & B_vs_C, …),

upsetly() will:

1. Compute all non-empty intersections across the set columns.
2. Keep only intersections with size at least min_intersection_size.
3. Optionally keep only the largest max_n_intersections intersections.
4. Draw:
   • Left bar chart: size of each set.
   • Top bar chart: size of each intersection.
   • Bottom dot matrix: which sets are present in each intersection.
5. Build rich tooltip text for each intersection, including:
   • Intersection name (e.g. A_vs_B & B_vs_C)
   • Intersection size
   • Members (element IDs), wrapped onto multiple lines.

In HTML output, you can also display the full tooltip text in a separate box which supports copy‑and‑paste.

Quick example

library(upsetly)

set.seed(1)
df <- data.frame(
  gene = paste0("g", 1:100),
  A = rbinom(100, 1, 0.3),
  B = rbinom(100, 1, 0.4),
  C = rbinom(100, 1, 0.2),
  stringsAsFactors = FALSE
)

p <- upsetly(
  x = df,
  set_cols = c("A", "B", "C"),
  id_col = "gene",
  max_n_intersections = 50,
  members_per_line = 10
)

p  # interactive plotly widget

This works in a regular RStudio viewer (or browser) as an interactive UpSet plot.

Using in Quarto / R Markdown with a copyable text box

To make the tooltip text (Intersection, Size, Members, etc.) easy to copy, you can add a small HTML element with id members_box and let upsetly() sync to it.

Example Quarto document

---
title: "upsetly demo"
format: html
---

```{r}
library(upsetly)
```
```{r}
set.seed(1)
df <- data.frame(
  gene = paste0("g", 1:100),
  A = rbinom(100, 1, 0.3),
  B = rbinom(100, 1, 0.4),
  C = rbinom(100, 1, 0.2),
  stringsAsFactors = FALSE
)

upsetly(
  x = df,
  set_cols = c("A", "B", "C"),
  id_col = "gene",
  max_n_intersections = 50,
  box_id = "members_box",
  members_per_line = 10
)
```
```{=html}
<pre id="members_box" style="
  border: 1px solid #ccc;
  padding: 8px;
  min-height: 120px;
  white-space: pre-wrap;
  font-family: monospace;
"></pre>
```

Interaction behavior

In the rendered HTML:

• Hover over an intersection bar:
  • The tooltip appears as usual.
  • The full tooltip text (Intersection, Size, Members, …) is also written into #members_box.
• Single click on a bar:
  • The current text is written into #members_box and locked.
  • Moving the mouse to other bars will not change the box content.
• Double click on the plot background:
  • The lock is released and the box is cleared.
  • You can then hover/click another bar to update again.

The content of members_box is pure text, so you can select and copy it easily.

Key arguments

upsetly(
  x,
  set_cols = NULL,
  id_col = NULL,
  min_intersection_size = 1,
  max_n_intersections = NULL,
  point_size = 8,
  bar_color_sets = "black",
  bar_color_inters = "black",
  active_color = "black",
  inactive_color = "lightgray",
  line_color = "black",
  title = "UpSet (plotly)",
  height = 500,
  width = NULL,
  members_per_line = 20,
  box_id = NULL
)

• x: data frame containing set columns and optional ID column.
• set_cols: character vector of column names that define sets.
• id_col: column name for element IDs (e.g. genes). If NULL, a numeric .elem_id is created.
• min_intersection_size: minimum number of elements for an intersection to be kept.
• max_n_intersections:
  • Limits how many intersections are kept (largest first).
  • Also limits how many member IDs are shown for each intersection in the hover tooltip for compatibility with earlier versions; synchronized box content remains complete.
• members_per_line: how many member IDs to show per line in the tooltip / text box.
• box_id: optional HTML element ID used for synchronized, copyable intersection details.
• point_size: dot size in the dot matrix.
• Color and layout arguments allow customization of bar colors, dot colors, and overall size.

License

MIT © 2026 Anbunensi